# This file is the result of combining several RDB files, specifically # T0374.t04.dssp-ebghstl.rdb (weight 1.53986) # T0374.t04.stride-ebghtl.rdb (weight 1.24869) # T0374.t04.str2.rdb (weight 1.54758) # T0374.t04.alpha.rdb (weight 0.659012) # These files were combined by translating their predictions into EHL # predictions with tables generated by compare-real, and then combining # those predictions with weights proportional to their mutual information # with the EHL alphabet. The comments from the individual files follow. # # Comments from T0374.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0374 # Using neural net t06-IDGaaH13-3-13-7-13-9-13-11-ebghstl-dssp-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0374.t04-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 2157 # # ============================================ # Comments from T0374.t04.stride-ebghtl.rdb # ============================================ # TARGET T0374 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghtl-stride-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0374.t04-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 2157 # # ============================================ # Comments from T0374.t04.str2.rdb # ============================================ # TARGET T0374 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-str2-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0374.t04-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 2157 # # ============================================ # Comments from T0374.t04.alpha.rdb # ============================================ # TARGET T0374 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-alpha-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0374.t04-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 2157 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1406 0.0087 0.8508 2 Q 0.5095 0.0090 0.4815 3 L 0.7340 0.0065 0.2594 4 S 0.8377 0.0064 0.1559 5 H 0.7905 0.0064 0.2031 6 R 0.6500 0.0108 0.3392 7 P 0.3707 0.0127 0.6166 8 A 0.1664 0.0169 0.8167 9 E 0.1059 0.0167 0.8775 10 T 0.0136 0.6048 0.3816 11 G 0.0194 0.4915 0.4892 12 D 0.0277 0.5362 0.4361 13 L 0.0071 0.9150 0.0779 14 E 0.0061 0.9236 0.0703 15 T 0.0068 0.9261 0.0671 16 V 0.0123 0.8999 0.0878 17 A 0.0122 0.7559 0.2320 18 G 0.0192 0.5314 0.4494 19 F 0.0365 0.2795 0.6840 20 P 0.0525 0.3554 0.5921 21 Q 0.0388 0.4250 0.5362 22 D 0.0679 0.4108 0.5213 23 R 0.0252 0.6972 0.2776 24 D 0.0305 0.7096 0.2599 25 E 0.0435 0.7281 0.2284 26 L 0.0706 0.6624 0.2669 27 F 0.1145 0.4928 0.3927 28 Y 0.1431 0.2889 0.5680 29 C 0.1429 0.1421 0.7150 30 Y 0.0965 0.0682 0.8353 31 P 0.0450 0.3311 0.6239 32 K 0.0359 0.3865 0.5776 33 A 0.0569 0.3476 0.5955 34 I 0.0953 0.1893 0.7155 35 W 0.0824 0.0843 0.8333 36 P 0.0753 0.1490 0.7757 37 F 0.1118 0.0933 0.7948 38 S 0.0752 0.1009 0.8239 39 V 0.0047 0.9547 0.0405 40 A 0.0046 0.9603 0.0351 41 Q 0.0047 0.9606 0.0347 42 L 0.0047 0.9591 0.0362 43 A 0.0047 0.9545 0.0408 44 A 0.0053 0.9216 0.0732 45 A 0.0063 0.8681 0.1256 46 I 0.0209 0.7456 0.2335 47 A 0.0267 0.4604 0.5129 48 E 0.0196 0.2766 0.7038 49 R 0.0273 0.1274 0.8453 50 R 0.0991 0.0496 0.8513 51 G 0.3008 0.0223 0.6769 52 S 0.8003 0.0077 0.1921 53 T 0.9201 0.0035 0.0764 54 V 0.9294 0.0034 0.0672 55 A 0.9248 0.0038 0.0714 56 V 0.9007 0.0046 0.0947 57 H 0.7253 0.0149 0.2597 58 D 0.0507 0.0174 0.9319 59 G 0.0384 0.0316 0.9300 60 Q 0.8004 0.0085 0.1911 61 V 0.9231 0.0030 0.0739 62 L 0.8739 0.0177 0.1085 63 G 0.9152 0.0043 0.0805 64 F 0.9221 0.0034 0.0746 65 A 0.9096 0.0050 0.0854 66 N 0.9003 0.0045 0.0952 67 F 0.8568 0.0144 0.1289 68 Y 0.7752 0.0204 0.2044 69 Q 0.6899 0.0346 0.2755 70 W 0.4451 0.0645 0.4904 71 Q 0.3054 0.0737 0.6209 72 H 0.1575 0.0780 0.7645 73 G 0.1039 0.0555 0.8406 74 D 0.1594 0.0704 0.7702 75 F 0.6036 0.0742 0.3221 76 C 0.7819 0.0439 0.1742 77 A 0.8637 0.0209 0.1154 78 L 0.8785 0.0185 0.1029 79 G 0.7153 0.0591 0.2256 80 N 0.7446 0.0383 0.2171 81 M 0.8205 0.0316 0.1479 82 M 0.8427 0.0213 0.1360 83 V 0.6969 0.0248 0.2783 84 A 0.2165 0.0255 0.7580 85 P 0.0129 0.6568 0.3303 86 A 0.0102 0.6837 0.3061 87 A 0.0204 0.7083 0.2713 88 R 0.0327 0.4100 0.5572 89 G 0.0277 0.2103 0.7619 90 L 0.0411 0.3311 0.6278 91 G 0.0411 0.5737 0.3851 92 V 0.0112 0.9003 0.0885 93 A 0.0047 0.9575 0.0378 94 R 0.0047 0.9611 0.0342 95 Y 0.0047 0.9610 0.0344 96 L 0.0047 0.9597 0.0356 97 I 0.0047 0.9610 0.0344 98 G 0.0046 0.9614 0.0340 99 V 0.0046 0.9605 0.0349 100 M 0.0047 0.9593 0.0361 101 E 0.0047 0.9598 0.0355 102 N 0.0047 0.9576 0.0377 103 L 0.0048 0.9545 0.0407 104 A 0.0048 0.9473 0.0479 105 R 0.0051 0.9231 0.0718 106 E 0.0063 0.8495 0.1443 107 Q 0.0100 0.6527 0.3373 108 Y 0.0558 0.2025 0.7418 109 K 0.0551 0.0526 0.8923 110 A 0.1507 0.0403 0.8091 111 R 0.2249 0.0572 0.7179 112 L 0.7997 0.0100 0.1903 113 M 0.8987 0.0045 0.0968 114 K 0.9228 0.0036 0.0736 115 I 0.9144 0.0049 0.0808 116 S 0.8704 0.0078 0.1218 117 C 0.7662 0.0203 0.2135 118 F 0.3932 0.0618 0.5450 119 N 0.1528 0.1866 0.6606 120 A 0.0663 0.2616 0.6721 121 N 0.0431 0.4136 0.5433 122 A 0.0073 0.9033 0.0894 123 A 0.0047 0.9475 0.0478 124 G 0.0048 0.9545 0.0408 125 L 0.0047 0.9604 0.0349 126 L 0.0047 0.9593 0.0361 127 L 0.0047 0.9590 0.0363 128 Y 0.0047 0.9567 0.0386 129 T 0.0050 0.9517 0.0433 130 Q 0.0061 0.9116 0.0823 131 L 0.0420 0.4712 0.4868 132 G 0.0418 0.0327 0.9254 133 Y 0.0874 0.0191 0.8935 134 Q 0.3970 0.0224 0.5806 135 P 0.5686 0.0538 0.3776 136 R 0.5086 0.1018 0.3896 137 A 0.4925 0.0738 0.4337 138 I 0.5609 0.0580 0.3811 139 A 0.4751 0.1072 0.4177 140 E 0.4475 0.1647 0.3878 141 R 0.4705 0.1325 0.3970 142 H 0.5374 0.0611 0.4015 143 D 0.1344 0.0300 0.8356 144 P 0.0231 0.1178 0.8591 145 D 0.0469 0.0293 0.9238 146 G 0.0543 0.0354 0.9103 147 R 0.2807 0.0179 0.7014 148 R 0.7907 0.0096 0.1997 149 V 0.8061 0.0159 0.1781 150 A 0.8082 0.0343 0.1575 151 L 0.8755 0.0170 0.1076 152 I 0.8821 0.0191 0.0987 153 Q 0.8770 0.0204 0.1026 154 M 0.8031 0.0260 0.1709 155 D 0.6237 0.0422 0.3341 156 K 0.3420 0.0332 0.6247 157 P 0.2157 0.0390 0.7452 158 L 0.1220 0.0472 0.8308 159 E 0.0628 0.0204 0.9167 160 P 0.0304 0.0725 0.8971